For some reason, newer versions of qt fail to build because they cannot
find certain system libraries such as libatomic and libdl.
Leaving the qmake compiler set to gcc seems to fix the problem.
Fixes#13221
* DataSpaces: 1.8.0
Add a newer release of DataSpaces for ADIOS2.
Also add missing `-fPIC` flags since this is a static library.
* ADIOS2: Dataspaces, libffi, libfabric
Add missing dependencies to ADIOS2. Without explicit control,
those dependencies might get picked up from the system environment
and will cause unstable builds.
* Hide transitive SST dependencies
* ADIOS2: Simplify SST CMake Flags
As proposed by Chuck
* Methods setting the environment now do it separately for build and run
Before this commit the `*_environment` methods were setting
modifications to both the build-time and run-time environment
simultaneously. This might cause issues as the two environments
inherently rely on different preconditions:
1. The build-time environment is set before building a package, thus
the package prefix doesn't exist and can't be inspected
2. The run-time environment instead is set assuming the target package
has been already installed
Here we split each of these functions into two: one setting the
build-time environment, one the run-time.
We also adopt a fallback strategy that inspects for old methods and
executes them as before, but prints a deprecation warning to tty. This
permits to port packages to use the new methods in a distributed way,
rather than having to modify all the packages at once.
* Added a test that fails if any package uses the old API
Marked the test xfail for now as we have a lot of packages in that
state.
* Added a test to check that a package modified by a PR is up to date
This test can be used any time we deprecate a method call to ensure
that during the first modification of the package we update also
the deprecated calls.
* Updated documentation
From Python docs:
--
'surrogateescape' will represent any incorrect bytes as code points in
the Unicode Private Use Area ranging from U+DC80 to U+DCFF. These
private code points will then be turned back into the same bytes when
the surrogateescape error handler is used when writing data. This is
useful for processing files in an unknown encoding.
--
This will allow us to process files with unknown encodings.
To accommodate the case of self-extracting bash scripts, filter_file
can now stop filtering text input if a certain marker is found. The
marker must be passed at call time via the "stop_at" function argument.
At that point the file will be reopened in binary mode and copied
verbatim.
* use "surrogateescape" error handling to ignore unknown chars
* permit to stop filtering if a marker is found
* add unit tests for non-ASCII and mixed text/binary files
Provide up to date specs for build options
Remove non-production versions
Format using autopep8 and flake8
Separate cmake options in adios2 2.4.0 version
Keep default as True as much as possible
Support for Python 2 and 3 for adios2 versions <= 2.4.0
Starting v2.5.0 only Python 3 is supported
Addressing review suggestions
* Add new ACTS releases
* Update ACTS dependency requirements
* We can actually be more specific here
* The material plugin is gone as of ACTS v0.10.0
* Add 0.10.4 release
* Remove material mapping plugin
It was merged into core as of 0.10.x, and given ACTS' youth it is unlikely to have actual users at this point in time.
* Minor clean-up of package information.
* Add variants, fix dependencies, and add conflicts for compilers that do not support C++17.
* Correct dependency type for CMake.
- Add a test that verifies checksums on all packages
- Also add an attribute to packages that indicates whether they need a
manual download or not, and add an exception in the tests for these
packages until we can verify them.
Some packages had incorrect checksums because they needed to be
downloaded from a new place or the package needed tweaking somehow.
These packages to sha256 and the new checksums have been verified by
fetching over https.
These packages have either been retired or are no longer retrievable from
any site we can find. They also aren't needed by other packages, so we're
removing them from Spack.
- allinea-reports: is now arm performance reports
- globus-toolkit: retired, globus is now a paid service.
- uberftp: used globus-toolkit, github site is retired.
- mpiblast: site is dead; no longer fetchable.
- py-mxnet: site and github are gone
- soap2, soapindel, soapsnp: site is gone, unfetchable
- arlecore: could not verify md5 securely
We'd like to use a consistent checksum scheme everywhere so that we can:
a) incorporate archive checksums into our specs and have a
consistent hashing algorithm across all specs.
b) index mirrors with a consistent type of checksum, and not one that
is dependent on how spack packages are written.
- [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
* py-line-profiler: add 2.1.2, re-run cython if needed
See rkern/line_profiler#166.
* Update var/spack/repos/builtin/packages/py-line-profiler/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Addition of 1.1.3 and 1.1.4
* Addition of conditional enum-34 installation.
* Update var/spack/repos/builtin/packages/py-maestrowf/package.py
Addition of versioning for pyyaml.
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Addition of enum34 back to older versions 1.1.3 and below.
* adjust building of OpenFOAM 1806 and earlier
- spack now unpacks into spack-src, but earlier OpenFOAM versions
still expect particular directory names (eg, OpenFOAM-v1806).
Resolve by creating a symlink during patching.
* replace openfoam 1806 patch with URL version
* fujitsu-mpi: commit new package
* Add homepage.
* * Modified the MPI commands to a simple form.
* Unnecessary processing has been deleted.
* Add conflict for all compilers except the Fujitsu compiler.
* Fix typo.
* Delete versions.
* Delete conditions for specifying the Fujitsu compiler.
* fftw: grouped precisions in a single variant
* fftw: simd options are now based on target features and not on variants
* fftw: simplified computing the selected precisions
* fix ipykernel dependency, newer versions are python3-only
* Update var/spack/repos/builtin/packages/py-ipykernel/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-ipykernel/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
Dotkit is being used only at a few sites and has been deprecated on new
machines. This commit removes all the code that provide support for the
generation of dotkit module files.
A new validator named "deprecatedProperties" has been added to the
jsonschema validators. It permits to prompt a warning message or exit
with an error if a property that has been marked as deprecated is
encountered.
* Removed references to dotkit in the docs
* Removed references to dotkit in setup-env-test.sh
* Added a unit test for the 'deprecatedProperties' schema validator
* libint: switch to 2-stage build for 2.6.0+
* libint: add tune and fortran variants
* cp2k: add support for libint >= 2.0
* cp2k: use pkg-config for linking libxc
* github releases are not released versions, but from-source
releases
* they lack the mimification of the JS/CSS components and as
such require node-js and npm, this conflicts with python@3:
* this commit
* drops the from-source dependencies on node-js and npm and
* updates the checksums to the correct sha256 hashes of the
pypi releases. The pypi-tarballs are different
* ZFP: CMake Package
ZFP is primarily build via CMake, which will have all install logic
and configuration files generated.
The 0.5.0 release did not support this yet, so we toss it.
* Patch ADIOS1: ZFP 0.5.1+ support
* ZFP: Expose all CMake variants
* new package: py-python-ldap
* fix dependency types
* improvements
* Update var/spack/repos/builtin/packages/py-python-ldap/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-python-ldap/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add openldap dependency
* go-md2man: disable module-mode
* Update var/spack/repos/builtin/packages/go-md2man/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* add singularity 3.4.1
Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>
* revert some changes
Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>
* add maintainers list to pkg singularity
Add @alalazo and me to the Singularity maintainers list
* Update var/spack/repos/builtin/packages/singularity/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/singularity/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/singularity/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
7bcb306 updated setup_environment in the GCC package to examine the
bin/ directory to find alternatively-named instances of CC, but this
failed to account for when GCC was being installed and failed when
it attempted to list the not-yet-existing installation prefix. This
commit updates the logic to skip this search if the bin/ directory
doesn't exist.
* libaio: fixed a condition that checks whether we are running on OS X
* libaio: simplified package by adding an explicit conflict for darwin
* libaio: added information to the docstring
* fio: added version 3.16, added conflict when using libaio, docstring
* lvm2: conflict due to libaio dep, improved docstring, simpler install
* mariadb: conflict due to libaio dep, improved docstring, version 10.4.7
* mariadb: the dependency on libaio is now conditional, removed conflict
* mariadb: fixed a typo in previous commit
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* libaio: turned into a MakefilePackage
Unlike the compiler binary name search logic, the `setup_environment` in
GCC's package assumes the compiler names are *exactly* `gcc`, `g++`,
etc. In many external installations (Homebrew, Macports) the
installation includes only *suffixed* versions such as `gcc-9`.
This patch uses the GCC compiler search suffixes to actually locate the
correct filenames for the installed compilers, allowing the
Spack-generated module file to have useful definitions of CC, CXX, etc.
It also allows for the possibility that the user's external installation
of GCC is compiled without Fortran support, in which case the `FC`
environment variables are not defined.
* The perl-uri-escape package duplicates perl-uri
The Perl URI::Escape module is in the Perl URI package so the Spack
perl-uri-escape package is a duplicate of the perl-uri package. This PR
does the following:
- replace `depends_on('perl-uri-escape')` with `depends_on('perl-uri')`
in packages that dependend on perl-uri-escape
- add the version from perl-uri-escape to perl-uri
- remove the unneeded dependency from perl-uri
- remove the perl-uri-escape package
* Reinstated perl-test-needs dependency
Put the perl-test-needs dependency for perl-uri back in but set it to
type='test'.
* For tests to succeed the type must be ('build', 'test')
Now that Spack injects microarchitecture specific optimizations for
the selected target, packages should avoid adding flags that could
step over those.
This PR adds interproscan-4.8, which has a completely different build
system than version 5. Note that this builds for running on a host as
opposed to a queue system. I am fairly certain that a queue system can
be configured later.
This PR also adds a patch for intrproscan-5 to build when the user
building the packages has a large GID by setting posix mode for tar.
* llvm: fixed issues with syntax and formatting
* use spec.architecture.target.family
* use spec.target instead of spec.architecture.target
* mesa: use == instead of __contains__
A function added to this package ran as part of importing it and
printed a warning for most Spack invocations, this removes the
warning message.
Also:
* Use compilers directly instead of Spack compiler wrappers (since
references to the compiler are embedded in text and binary files
of the installation)
* Add 'cross' variant for setting CROSS environment variable for
build
* Set UPCXX_INSTALL for generated module files
* Set UPCXX_GASNET_CONDUIT/UPCXX_NETWORK in generated module files
on Cray systems
* Also set UPCXX_NETWORK in build environment for Cray systems
The following dependencies were added:
+ depends_on('perl-exporter-tiny', type=('build', 'run'))
+ depends_on('perl-list-moreutils-xs', type=('build', 'run'))
Seamless translation from 'target=<generic>' to either
- target.family == <generic> (in methods)
- 'target=<generic>:' (in directives)
Also updated docs to show ranges in directives.
Fixes#12829
This adds a variant to the util-linux package that controls whether it
builds its own libuuid. Variant defaults to True. It enables other
packages to choose to get libuuid from the libuuid package instead.
This also changes the cryptsetup package to build util-linux with
~libuuid (so it uses an explicitly-Spack-built instance of libuuid
instead).
- add missing perl dependency
- only filter Makefile if referred to dependency is in the spec
- rewrite the shebang line of scripts to use spack perl
- remove tabix dependency as tabix and bgzip are part of htslib
* cuda: New version 10.1.243
Adds CUDA 10.1.243. The installer command-line arguments have slightly
changed, hence in the install method the version needs to be inspected
in order to give the correct arguments for the new installer.
* cuda: Combine common command-line arguments
The CUDA 10.1+ installer has slightly different command-line arguments
than previous versions. Keep the common parts together and only split
where they are different.
* Make flake8 happy
* update py-bokeh: new version & dependencies
* Revert "update py-bokeh: new version & dependencies"
This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f.
* update py-bokeh: new version & dependencies
* trigger travis-ci
* adjust python dependency-type to br
* update py-bokeh: new version & dependencies
* Revert "update py-bokeh: new version & dependencies"
This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f.
* new package: py-fsspec: add package.py
* trigger travis-ci
* adjust python dependency-type to br
* CGNS: Add setting of RPATH on Darwin
This should go in the CGNS CMakeLists.txt, but it isn't there yet and won't be in previous versions, so best to handle it here.
If building on darwin/MacOSX, need to set the RPATH so applications can find shared library correctly.
* Restrict MACOSX_RPATH setting
This has now been added to the CGNS distribution, so the setting of `CMAKE_MACOSX_RPATH` should be restricted to current and previous releases and not upcoming releases.
* new package: py-configojb
* add version 4.7.2
* improve dependencies
* fix url for versions > 5.0.0
* Update var/spack/repos/builtin/packages/py-configobj/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-configobj/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* use format to create url strings
* fix typo
* improve style
* Update var/spack/repos/builtin/packages/py-configobj/package.py
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* py-gpaw: Fixing missing numpy include path, adding newer version of py-gpaw and fixing a bug with libxc.c in older py-gpaw
* py-gpaw: Fix Python and ASE version dependencies
- GPAW 19.8.1 requires Python 3.x, add dependency on python@3.5:
- GPAW releases are associated with a corresponding ASE release, add
matching ASE version dependencies.
* py-gpaw: Enable the scalapack variant by default
GPAW installation instructions say scalapack is optional but "highly
recommended". Thus enable it by default.
* add new cutadapt release 2.5, and adjust dependencies conditional on version
* use https, not ssh, for git url
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* update py-xopen (add 0.8.2 checksum)
* refine version specific dependencies
add py-bz2file, which needs to be created
* create py-bz2file
* Revert "refine version specific dependencies"
This reverts commit 70649da98851fefb2f936ca99a012fe6bef07b70.
* Revert "update py-xopen (add 0.8.2 checksum)"
This reverts commit 7400f44caa6e98419eb4bc3107704b91e8a2018b.
* update py-xopen (add 0.8.2 checksum)
* refine version specific dependencies
add py-bz2file, which needs to be created
* py-bz2file needed when built with python 2.7
Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
* space after comma
- Fix trailing whitespace missed by the bug described in #12755.
- Fix other style issues that have crept in over time (this can happen
when flake8 adds new checks with new versions)
There are problems with libunwind for arm and trying to use it with mesa.
See for example:
https://github.com/grate-driver/mesa/issues/6
disabling use of libunwind for arm, allows the package to be built
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
